Chuck vs The CIA
by intermittentdarkness
Summary: After being locked away for three years by the CIA, Casey and Sarah come to break him out, but Chuck is not the same.
1. Chapter 1

**A/N**: I haven't written anything in a while, and so this might be terrible.

**Disclaimer:** NBC owns everything. You know this.

For the first few weeks, Chuck tries to remember everything about Sarah – her long, blonde hair, her perfume, her smile.

After six months, he forgets the sound of her voice.

After a year, he forgets her smile.

And after three years, he can only remember her long, blonde hair. And this is why when Sarah knocks down the door, with Casey quickly following, he just stares.

"Chuck?," Sarah whispers, tears clinging to her eyes. "It's me, Sarah." She reaches her hand up to cup his face, and he jerks away roughly. This only spurs her tears forward and Chuck only manages to get out two words before he inevitably joins her: "Get. Out."

She stares uncomprehendingly at him, and Chuck can only glare at her, hoping to get his point across. Sarah runs quickly to the bathroom, slamming the door behind her.

Casey looks at Chuck like he's insane, but in true Casey fashion, asks bluntly, "You wanted me over _her_? Why the hell would you want me?"

"You're not crying," Chuck states simply.

"Oh." Casey nods.

"I know it's not fair, but I just can't deal with her shit right now."

Another nod.

"Can I see my sister now?," asked Chuck hopefully.

Casey didn't meet his eyes as he quickly changed the subject. "We need to get you out of here kid, pronto. We didn't exactly get permission to extract you." He sighs, "Chuck, they never would have let you go."

Chuck, of course, realized this truth a long time ago, when the smell of Sarah's peach perfume was still a faint memory.

"And," Casey continues, "The first place the CIA will look for you is Ellie's apartment."

"Oh. I see. So the plan is to what, outrun the goddamn CIA?," asks Chuck, his tone bitingly sarcastic.

To say that Casey looks shocked is an understatement, but apparently Sarah finally stopped crying, stumbling into the tense room.

He knows she wants to say how sorry she is, to tell him how much she missed him, loves him, but he just can't hear it right now.

He can't stay in this room any longer, so he says the only thing he can. "Let's go."

The car ride is as awkward as can be expected, with Casey's hand never quite leaving his gun, and Sarah's eyes watering whenever she looks at him. But soon they're there, wherever there is, and Casey delivers instructions that Chuck thought he would never hear again.

"Stay in the car."

Chuck laughs, starting out as a quiet chuckle, before turning into maniacal laughter. He knows that Casey thinks he's snapped, but he can't dispel his fears because it's just _so funny_.

Casey reluctantly leaves him alone a minute after he finally stops, and Chuck is glad that Sarah can't see him like this, or the waterworks would start again.

Looking around, Chuck is startled by the realization that he has no idea where he is. After the rough agent bagged and tagged him, he was sure that the pilot went at least in two complete circles, making it impossible for him to ever gather his bearings.

But Casey is back before he can get a good look around, roughly pushing him into the – well, it looked like a normal suburban house. He is shoved onto a pretty beaten couch, and he can't help but observe that his CIA-provided prison was better than this crapshack. He stifles a giggle, not wanting to set Casey off, who is still worriedly glancing at him.

He opens his mouth to speak, but Casey only glares at him. Sarah comes striding into the room, and Casey immediately rushes outside, probably to escape the awkward reunion.

"Chuck," she starts. "I – "

He cuts her off. "I know." He actually doesn't _know_, but he can guess, and he doesn't want to hear it.

But super secret agent Sarah knows better, and suddenly she's on her feet, staring at a spot above his head.

"No Chuck, you don't."


	2. Chapter 2

**A/N:** I'm crying now, after writing this. But, please try to stick it out, because now that Chuck's hit bottom, he can only go up. And I still don't own Chuck. Also, to all of my reviewers (both on LJ and thanks so much! I'm not going to address everyone's concerns, but I will touch on some of them.

Will this be Chuck/Sarah?: Yes.

It's moving a little fast: Yeah, this probably won't be too long. Mostly because I've never stuck it out when I when I had huge plans for some epic novel. And honestly, I already know the ending, and I don't want to drag it on.

She's crying again, but whenever Chuck opens his mouth her tears subside enough for her to shoot a glare at him.

"Chuck," she starts again. "I know that you must feel betrayed. You probably think that I never looked for you, or looked hard enough. But, that's not true. I was just looking in the wrong place. Are you listening, Chuck?"

He steadily ignores her, and she repeats the question, sounding a little angry. Chuck manages a nod.

"We hacked through all the CIA files, we held people at gunpoint. Chuck, we even committed treason!"

His jaw drops as she continues, crying again. "It wasn't the CIA that had you. Someone must have found out you were the intersect, and intercepted you. And do to our…personal relationship, neither Casey or I were privy to your location. We didn't even know who had taken you until a few months ago. Casey and I had gone rogue, trying to find you. But Chuck, there's something else."

Still in shock, Chuck barely hears her continue. "We were going to be executed, Chuck. For treason. I would have gladly died for you, Casey, too, but if I did, then I wouldn't be able to take care of you once you were in CIA custody. Do you understand, Chuck?"

Chuck does understand. He understands that she was willing to give up everything for him. But what he truly understands is that he is merely trading one prison for another.

Sarah tries to force him to look at her, but Chuck's doing very well at looking anywhere but her face.

He feels a warm hand on his cheek, and he instinctively leans into it before he roughly flinches away. He sees her face crumble before she hastily exits, half-running to where Chuck knew Casey to be.

It's not that Chuck doesn't love Sarah anymore, but his memories of his time in that room are all jumbled thoughts of _her_. He isn't sure of anything anymore, least of all himself. Sarah still loves the man that he _was_, and can't accept that maybe he's not the same. He's so lost in his thoughts that he doesn't notice Casey walk back in.

"Still smooth as always, Chuck."

In the old days, Chuck would have responded with some witty comment. _We can't all be undercover lovers, Casey._ But back then, his entire emotional range didn't consist of blind anger.

Chuck is barely able to stop himself from glaring, which Casey takes as a sign to continue. "Aren't you going to yell at me too? Maybe punch me? Come on, Chuck." Casey spits out the last word, egging him on.

God, does he _want_ to hit him. The man represents everything wrong in his life, everything that would everbe wrong with his life. And, Casey knows he deserves it, too. Chuck's turned into the kind of person who takes his anger out on the people who least deserve it. He pictures Sarah, tears streaming down her red face, and his hands curl into fists despite himself.

Casey's on the floor, a red tinge spreading across his cheek before either of them realize what happened.

But Casey's fast, much faster than him, and now he's sporting a matching bruise.

"Ow!," he cries.

"What's the matter, Chuck?," Casey asks sarcastically. Jesus, he _wants_ Chuck to hit him.

And suddenly he rams into the sarcastic bastard, and for a few minutes he feels completely free, lost in a tangled web of pain and limbs. He idly wonders where the blonde hair came from, but barely registers the thought as he blindly reaches out to punch Casey in the stomach, only to discover he's not there.

Instead he hits something much smaller, much softer.

Oh god. _Sarah_.


	3. Chapter 3

**A/N:** This part is short, I know. But I'm a college student, and Calculus is a tiny bit more important than this.

To answer someone's question, there might be a character death, but it with be a _new_ character. I still haven't decided

I still don't own Chuck.

Casey grabs Chuck and roughly throws him on the couch, before going to help up Sarah. She seems to be fine - three years in solitary confinement didn't exactly improve his strength – but it's her expression that gets to him. She looks betrayed.

Sarah never betrayed him, and how does he repay her?

The silence in the small room is overwhelming. Chuck can't bear to look at her, but all she can seem to do is stare at him. Finally, she speaks. "What did they _do_ to you, Chuck?"

Ignoring his lack of a response, she continues in a soft voice, "I forgive you. I just never thought that you wouldn't be the same," as though she is to blame, not him.

Still not looking at her, Chuck let's out an anguished whisper, "Don't."

Sarah looks confused, but Chuck continues, "Don't blame yourself for something _I_ did. And please, don't forgive me."

Chuck finally raises his eyes to meet hers, and is so surprised to see only kindness in them that he just can't seem to tear his gaze away. "Are you okay?," he asks quietly.

She nods, tearing up again.

"When will they be here?"

"Soon," Casey answers coldly, obviously not as forgiving as Sarah.

Chuck nods, still not taking his eyes off of Sarah.

He sighs. "I missed you." He lets out a choked sob, before reining his emotions in. "I think… I think I was blaming you for everything. I mean, it makes no sense, but I had convinced myself that everything that had happened was because of you. And in a way, it was, I guess."

Sarah looks pained, so Chuck rushes to finish. "I mean, you were one of the best things in my life. You made me happy, even if it was all fake. When they locked me up in there, with really nothing to do – they didn't want me to flash on anything – all I had were my memories, and mostly I thought of you."

He nervously wrings his hands in his shirt, waiting for her response.

Chuck feels a warm hand lifting up his chin, and is greeted by Sarah's warm eyes. She moves her hand to cup his face, and he sighs. "God, Sarah, I'm sorry."

"I know." She entwines her other hand with his and gives him a small smile.

Casey coughs.

Part of Chuck wants to laugh, but one look at Casey's face makes him relive all that has just happened, and he wisely keeps his mouth shut.

Casey's low voice fills the room. "Fifteen minutes."

Not knowing what to expect, Chuck starts peppering Sarah with questions, causing her to roll her eyes at him. It's easy to fall back into their old rhythm, and Chuck almost forgets the last three years.

He's going to be taken to a holding cell for a few days, but it should be much nicer than the one the terrorists provided. From there, he'll be taken to apartment-style quarters, with all the amenities. Once he proves he's not a flight risk, he'll be allowed visitors. Sarah promises she'll come every day, and Casey grudgingly agrees to "maybe stop by."

It isn't perfect, but it's more that he deserves.


	4. Chapter 4

**A/N**:So, I'm really happy that I wasn't flamed. Everyone was so happy that Chuck and Sarah reconciled (including me). As for the question of how long this will be, this is chapter 4, and I'm sure that a few of you can start to sense 'the end is near'. There will definitely be two more chapters (maybe three – it depends on if I write Sarah in or not), and an epilogue. But my chapters are short, so it won't be very long.

Five agents arrive to collect him. Their eyes linger on him, obviously curious why _he_ would need protection. But it seems they're professionals, saying only a few words, not hinting at anything they might be thinking.

It's not rough like the last time, though he is blinded again.

Casey and Sarah are in another car, and the thick silence makes the minutes-long ride seem like hours. He's nervous, but tries to appear calm in front of these intimidating agents.

Soon he's being lifted by two strong arms out of the car and into a very cold building. He can hear the chatter stop, and he thinks this must be like on Alias, when Sark was dragged in.

He's quickly ushered through the room, and once the door clicks, his hood is lifted, and he has to blink a few times before he really sees anything. Immediately seeking out blonde hair, he is disappointed, but tries to keep his face blank.

He opens his mouth, but one of the agents glares at him. Another agent nods at the first, and then they start.

"It's safe to talk now. Do you know the plan?""Not exactly," Chuck remarks. A third agent quirks his eyebrow, but stays silent.

"You're going to be taken to a temporary detention facility," he speaks slowly, looking at Chuck for some sign of recognition.

Great. The agents think he's stupid. Chuck nods, wanting to get this over with.

"If it appears that your location is safe, you will be moved to more permanent housing." Another nod.

"You will be assigned a cover."

"A Cover?" Chuck repeats.

Annoyed now, the agent continues, "The housing is home to many old criminals. While they claim to have cut all ties with their past organizations, we must assume that some will be acting as double agents."

Wow. Chuck can't help but think that Alias was right.

"According to our superiors, _you_ are an asset and must be protected at all costs. Therefore, it is imperative that your identity be protected."

The third agent is staring at him curiously, now. "Do you understand?"

"Oh. Right," he responds distractedly. "So who am I?"

Seeming satisfied with Chuck's response, the first agent reads off a paper, "Charles Culling, Chuck. You were a third year student at Stanford, before you hacked into the CIA database and corrupted many of our higher-level documents, as well as recovered confidential information. Three agents brought you in, in suspicion of selling secrets to terrorist organizations. We are holding you until we can find otherwise."

They give him a moment, most likely to mull it over, but Chuck can only think about one thing. "I'm such a badass."

The third agent cracks up before schooling his face back into a detached façade. The other agents stare at him, before returning to Chuck.

Chuck's giddy in anticipation. He knows he should be upset, and he is, but this has been his life for years now.

And now, he's the _bad guy._ No more nerd herd – no more geek status. He's cool. It's his high school dream come to fruition.

Plus, Sarah would probably find it sexy. He would definitely beat Bryce now.

Chuck was still smiling, even when he was brought to a windowless cell, with only a rusted toilet for company.


	5. Chapter 5

**A/N:** I almost gave up on this story. I wrote an awful chapter, got exactly one review, and then got buried under insane amounts of work. But I'll finish this, even if it sucks. Please try to stick with me! I have a cool scene coming up!

Chuck's good mood soon wears off, and he finds his thoughts becoming darker with each passing second. He thinks of Sarah, her beautiful blonde hair, her sweet smile; how she couldn't help him, didn't love him enough –

He cuts his thoughts off. Sarah, he reminds himself, has protected him countless times. She's saved him.

And yet, he's still back in a cell. What's changed?

Wow. He's arguing with himself.

Chuckling, he runs a hand through his hair. Maybe he _has_ lost it.

His thoughts are interrupted by a deep cough. Turning around, he realizes that the agent has witnessed his madness. _Great_.

He grins sheepishly, trying to indicate his sanity. Unconvinced, the agent frowns, "Are you alright?"

Chuck nods, and tries to keep his voice as carefree as possible. "Erm, yeah. I was just thinking of something funny."

Quirking his eyebrows, the agent nods, still looking uneasy. "We're moving you."

"Now?" Chuck questions. "But they said – "

"Well," the agent starts, his face becoming flushed. "It seems that your _friend_, Agent Walker, was able to – expedite your relocation."

Chuck grins, realizing what he means. The agent cracks a smile, before quickly donning a blank expression.

The walk isn't too bad. He's handcuffed – for appearance – but it really doesn't bother him. If Sarah was able to get him moved, than certainly she will be there to see him moved.

Itching, he wiggles his nose in vain, before giving up.

He's brought through a park of all things, into what looks to be suburbia, with white gates, a perfectly mowed lawn – is this where he's living?

It's not alone either; the 'park' is surrounded by small, quaint-looking houses, each lined by a white picket fence.

It's like he's back in time.

He must have voiced his thoughts aloud, because the agent barks a laugh. "Well, this compound was created in the fifties. We used to house reformed KGB officers here. In fact, there are still a few here."

He opens the fence, before guiding Chuck forward. Once they're inside, his handcuffs are removed. Rubbing his sore wrists, he looks around hopefully. Sensing his disappointment, the agent mutters, "She got into a little trouble, but don't worry." Chuck nods, still slightly upset.

"Well, do you want the tour?" asks the agent enthusiastically.

It's a fully furnished one-bedroom, one-bath house, complete with digital cable. "Not all of 'em get all of this," the agent tells him. "But seeing as you haven't done anything…"

It's actually pretty nice – well, for a prison, anyways.

There's a knock at the door. It's Casey, looking extremely awkward, with a teddy bear in his hand.

He practically throws the bear at Chuck before placing a bag on the couch. "Sar – Agent Walker," he corrects himself, "sent me along with some things." Casey's eyes linger on the bear, his expression still uncomfortable.

"Uh… thanks," Chuck says weakly.

"She's coming by, later tonight, with some more stuff. I think it's a bunch of movies, things like that."

Chuck smiles to himself, before looking around and realizing that he has a full entertainment system.

Morgan should be here to see this – Morgan, who he will never see again. Morgan, who was hopelessly in love with his sister. _Ellie_.

The darkness claws at him again, and he struggles to not be pulled under.

Trying to distract himself, he looks through the bag Casey brought. A huge grin forms on his face as he realizes that Sarah knows all of his favorites.

Sarah joins him in the middle of his favorite western, snuggling into him without any hesitation.

Chuck wraps his arms around her and smiles.


	6. Chapter 6

**A/N:** Whoops. I suck. Flame me, because I deserve it. Only the epilogue left, and yes, it will be mostly corny. But there is an actual story…so….stay tuned.

After a month, Chuck falls into a routine. Shower, have breakfast with the Swiss hacker next door, once again fail to grasp the intricacies of football, have lunch with Sarah or Casey, and hang out with the other criminals at the recreational center for their approved "group time".

Occasionally an agent will show up under the pretense of questioning him, seeing if he will flash on various names and faces. He doesn't, but the visits are a nice way of breaking up the day.

Lately, Chuck's been distracted: one of his "neighbors" has disappeared. While he wasn't exactly close to the seven-foot-bulldozer, it doesn't comfort him to think that someone can be kidnapped from within CIA custody. His hacker friend, Adrien, says that this is pretty common; the large man was probably recruited into the agency.

"That happens?""Sometimes, man. If they can trust you. But judging by all those visits – they _definitely_ don't trust you."

Chuck blushes. "Is that what everyone thinks?""Actually, they think you're banging the blonde one."He's sure his face is tomato red as he manages a squeaky, "Oh?"

"You want me to tell them something else?" Adrien asks, surprised by Chuck's response.

"No, no," Chuck quickly replies, trying not to sound too desperate.

He really doesn't mind all the guys thinking that. The only problem is, now Sarah's going to kill him.

The rest of the day passes uneventfully.

Later that night, when Sarah joins him for dinner, he manages not to tell her about her new reputation, instead asking her about what Adrien said.

She chokes on her pasta. "You want to be an agent?""It's better than being stuck here all day."

Looking quite serious, she turns to face him. "Chuck," she pauses, "I don't want you to work for them. For us, I mean.""You don't want us to work together?" he asks, feeling hurt.

"Chuck," she soothes. "You know that's not what I meant. I just – It's too dangerous, alright?"

"Dangerous for who exactly? In case you haven't noticed, I'm kind of being held by the CIA, for my safety," he counters swiftly. "My life is over."

Sarah rolls her eyes. "Don't be so dramatic, Chuck."

"It is though. I'll never see Ellie or Morgan again. And I'm not even Chuck Bartowski anymore!," he finishes, his face flushed.

"I can't convince you to drop this, can I?" she whispered softly.

Giving her favorite crooked smile, he shakes his head.

Not looking at him, she adds, "I'll mention it tomorrow."

The next morning, Chuck is visited by the same agents that brought him in. His neighbors look at him curiously as he's escorted into the CIA building. Agents pause to stare before quickly resuming their tasks.

He's brought to a small conference room. The gray walls do nothing for his nerves, but he feels his spirits lift as Sarah walks in, followed by several other agents. But she won't look at him, so he stares directly at her, hoping to catch her.

So lost in his task, he missed the start of the meeting. A light cough brings him away from Sarah's face, into a much less attractive one.

"Mr. _Culling_," he stresses. "Do you know why you're here?"Trying to sound confident, Chuck manages a terse "Yes."

"Agent Walker has suggested that with your previous experience with CIA operations, as well as certain – _skills_ that you possess, we should consider bringing you on as an agent." The agent's raised eyebrows clearly convey _his_ thoughts on the matter.

Chuck nods.

"She has also brought up the fact that the CIA cannot hold you indefinitely, as you have committed no crime. For your safety, you will need to stay with the CIA, but I see no reason that you can't work here."

"As part of your cover," he continues, "You will be brought in as an asset, eventually becoming an analyst. We may decide later to have you become field-certified as well."

In shock, Chuck barely registers the agent's next words.

"When you go back tonight, act as though nothing has changed. Tomorrow you will be escorted for questioning. After an appropriate time, we will deem you 'safe' and will move you off the premises."

After somehow fooling his neighbors, Chuck falls into a restless sleep.


	7. Chapter 7

**A/N:** Well, its finished. I hope you all enjoyed reading it as much as I enjoyed writing it. Maybe I'll write more later, but obviously there will not be a sequel (though I guess with a little editing I could have.) This is most definitely _it_.

Five years later, Chuck leads a relatively normal life. Occasionally he dodges bullets, or runs from people who would shoot him, but Sarah is always there to protect him. And being with Sarah, he's practically a legend among his fellow analysts.

Things with Sarah have been never better. In fact, he's engaged to her. He still can't really believe it, but it seems more credible than any other aspect of his life.

Today, Sarah insists on setting up their registry. Why it is necessary is beyond him – after all, everyone they know is in the CIA, but Sarah's harsh glare has shut him up.

Seeing Sarah distracted by a wok set, he quickly walks out to a bench at the mall.

Rubbing his eyes tiredly, he watches Sarah through the store window. Knowing he has only a few minutes, he quickly pulls out his headphones and curls up on the bench. But before he can get them in his ears, he hears a familiar voice.

"Chuck?"

Barely remembering his painfully long and intensive training, Chuck freezes. _Always deny who you are. _

Trying not to arouse the man's suspicion, he slowly rises from the bench and starts to head back to the store. If he can convince him that he's just seeing things…

"Chuck?" another voice, feminine this time, calls. Obviously flustered, she glares at him, before launching into a rant about silverware and woks, and Chuck wishes he knew Morse code, because if Morgan sees them together they're screwed.

"Oh my god, Sarah!"

_Shit._

Chuck sighs as Sarah turns sharply, immediately switching into her alter ego.

Sarah quickly grabs Chuck's hand, dropping all her bags on the floor in the process. He knows that she's reaching for her gun with her other hand, so Chuck rushes in to distract Morgan.

Morgan's face is white, but his stance is strong, confident. Chuck should have realized that after eight years even Morgan would change.

"Hey, buddy," he tries, in a lighthearted voice. It sounds fake, wrong, and Morgan blanches.

Opting for a different strategy, he soothes, "It's okay. It's alright. I'm okay."

Morgan's face crumples, and falls uneasily into Chuck's arms, sobbing into his shirt.

Chuck only hears fragments - "thought you were dead", "where did you go", "eight years" – but they're enough. He knows it's unfair, but he's glad Morgan missed him too.

Sarah looks devastated, but whispers, "We've got to get him out of here." Peering around, Chuck sees that they have indeed caused quite a scene.

He nods and lets Morgan lean on him as they walk in silence.

They stop in a restaurant, and force Morgan to eat as Chuck downs a beer.

Then Morgan begins peppering them with questions.

"Where did you go? You died, and you – Sarah, you just…disappeared! Why would you do that?"

Seeing no other option, Chuck tells him the truth. Everything, starting with Bryce, until that very morning. Sarah's angry, but Chuck just shakes his head and continues.

"And today, buddy, we were going shopping, because we're getting married," he ends with a smile.

Raising his eyebrows at Morgan's blank expression, Chuck orders another round of beers.

Finally entering the conversation, Morgan whispers, "Wow. You're totally badass."

Chuck can't help it. He laughs for what feels like hours, until there are tears streaming down his face.

"Yeah," he mutters. "I guess I am."

"So you – and Sarah – are _agents_?" Morgan asks incredulously.

They both nod.

"Dude!"

They spend the rest of the night reminiscing. When Morgan leaves to go to the restroom, Chuck accompanies him, not wanting to be a part of the next step. Morgan's asleep fifteen minutes later, which Sarah quickly explains away by all the beers.

They find Morgan's house – the same as before. Chuck carries Morgan to the door while Sarah scouts out the surroundings. As gently as possible he lays Morgan in bed, as Sarah brings out a glass and a bottle of vodka and places them on the nightstand. He won't remember the last twenty-four hours, but he'll have a nasty hangover.

Sarah holds his hand while Chuck calls in the incident.

"We'll finish the registry tomorrow," he tells her, sparing her a small smile.

And they do. They're married six months later. Sarah gets pregnant one year after that, and Chuck is field-certified after another four months. He's shot on his first assignment and wakes up to his wife and son by his side.

And together, they try to have a life as boring as possible.

THE END


End file.
